DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences

The φ3T DNA methyltransferase (Mtase) and most of the SPβ Mtase genes have been sequenced. With the exception of their promoters, no difference was found between the φ3T and SPβ Mtase genes which code for an enzyme with a M r of 50 507, consisting of 443 amino acids (aa). Comparison of the deduced aa sequence of the φ3T/SPβ type Mtase (target specificity: GGCC and GCNGC) with that of the previously established sequence of the SPR Mtase (Buhk et al., 1984) which has the target specificity GGCC and CCGG, reveals strong similarities between these two types of enzymes. There is, however, one striking difference: both the φ3T/SPβ and the SPR enzymes contain at different positions inserts of 33 aa, which have no homology to each other. We suggest that the methylation specificity unique to each of the two types of Mtases (GCNGC in φ3T/SPβ; CCGG in SPR) depends on these inserts, while the GGCC-specific modification potential common to all Mtases is determined by structures conserved in both types of enzymes. A DNA fragment of non-modifying phage Z, which shows homology to both flanks of the SPR Mtase gene, was also sequenced. This segment can be described as a derivative of SPR DNA, in which the Mtase gene and sequences at its 5' end have been deleted, with the deletion extending between two direct repeats of 25 bp.